Bioinformatics Approach in Enzymology: Molecular Structure and Data Analysis

Your instructor: Angel Herráez, PhD - University of Alcalá (Spain)

short URL:   http://bit.ly/DEU2014

The icon points to handouts that either will be covered during the workshop or you can use as support reading during your study.

Brief outline of the workshop schedule (pdf).

Student assignment:
  Instructions for your personal work and your mini-project. (pdf)
  Listing of proteins.

Section 1

Molecular and structural approach of enzymes and their interaction with substrates, effectors and inhibitors. Application of molecular visualisation for investigation of the active site, the structural bases for substrate recognition, and catalytic mechanisms. Analysis of enzyme-ligand contacts.

By the end of this first session, each student should choose a protein of interest to start practicing up to next session. Think of a mini-project around that protein, that will consist on investigation and presentation of structural/biologically relevant features.

• Introduction to MolVis software and Jmol. Retrieval of (macro)molecular structure data (Protein Data Bank, at www.pdb.org).
  • Presentation of resources (PDB, PDB101, Molecule of the Month, Proteopedia, CACTUS, Jmol-Direct, DIY-molecules, PubChem).
• Presentation of Jmol.
• Download and use Jmol (www.jmol.org): general actions for rendering the molecules in diverse ways.
• Demonstration and practice with examples.
• How to load molecular structure files.
• Use of the mouse.
  • Mouse help document :: Türkçe
• Use of the pop-up menu in Jmol to obtain information and to adjust the rendering style.
• Capturing images (both static and animated).
• Saving results from Jmol.
  • Saving files from Jmol
• Use of the Jmol Console and commands relevant to investigation of ligand-protein interaction.
  • How to access the console.
  • Practice exercise: citrate synthase monomer 6csc.pdb
  • Try now with e.g. Aricept™ bound to acetylcholinesterase, 1eve.pdb (donepezil hydrochloride, for Alzheimer's disease)
  • Try with a protein-ligand complex of your interest
• Using script files to store and reuse frequent series of commands.
• Jmol Scripting Documentation - the ful manual

Section 2

Fundamentals leading to further understanding of pharmacological issues and drug design strategies.

• Examples:
  • Cyclooxygenase-1 (COX-1, prostaglandin H2 synthase) complexed with different nonsteroidal antiinflammatory drugs (NSAID)
  • Dihydrofolate reductase complexed with different antifolate drugs
• Analyse distribution of polarity.
• Binding pockets: molecular surfaces to display shape and pockets.
  • Practice with surfaces
• The ligand view in PDB website:
  • Formula (image).
  • 3D model.
  • Other protein structures that have the same ligand.
  • View interactions:
    • Images
    • Ligand Explorer (another software, using Java Web Start)
    • View interactions in Jmol (contacts) :: "View Pocket in Jmol".
• Contacts, interaction of different kinds: the contact command in Jmol.
  • Practice with contacts
  • Interactive Visualization of Intermolecular Contacts by Hanson & Wyatt, presents details and excellent examples on uses of the contact command.
• Go back to study the examples

Make a decision on your mini-project.

Section 3

Technical tutorial on how to implement molecular displays within a presentation in order to illustrate and discuss the above issues.

• Direct use of Jmol application with your files prepared in advance.
  • See Saving files from Jmol
• (no) Implementation in a Proteopedia page.
  • See Proteopedia or other platforms
  • Option for offline version.
• (no) Authoring a webpage using the Export to Web module in Jmol.
  • See E2W

Section 4

Simulations in the computer as a tool for teaching enzyme kinetics and for students independent work: understanding the meaning of K_m and V_max, effect of inhibitors, graphical plots …
Advanced data analysis in enzyme kinetics. Enzymatic kinetics, inhibition and types. The use of the linear transforms vs. nonlinear regression for data analysis.

• Available at biomodel.uah.es/en/metab/
• Simulators
  • A) Graphical analysis, M-M
    • Perceiving the meaning of K_m and V_max parameters
  • B) Linearised plots
    • Comparison of the plots
    • Effect of experimental error
    • Reliability of parameter estimation on linear plots
  • C) Enzyme concentration
    • Influence of enzyme concentration
    • Perceiving the meaning of the k_cat parameter
  • D) Cooperativity
    • Graphical meaning of the Hill coefficient
• Design quizzes or activities that require the use of the simulators, in order to foster comprehension.
• Nonlinear regression utility for M-M data analysis
  • Promote the use of nonlinear regression, which is long recognised as a better choice for data analysis and is now accessible.

Section 5

Student presentations on their practice work on display and discussion of enzyme-ligand interaction.

• Presentation of the mini-projects